MERFISH Report

1. Overview

1.1 Sample Information

A brief sample information is generated from the submission table for the following analysis.

Sample Index and Basic Information
Batch Index Genotype Data Path region
1 009GFPcre GFPcre 202402181603_20240218Julio011n009VZG191m500x01_VMSC00101 region_1
1 011GFP GFP 202402181603_20240218Julio011n009VZG191m500x01_VMSC00101 region_0
2 724GFP GFP 202402181602_20240218Julio724n008VZG191m500x02_VMSC05201 region_1
2 008GFPcre GFPcre 202402181602_20240218Julio724n008VZG191m500x02_VMSC05201 region_0

1.2 MERSCOPE Data Quality Summary

The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.

Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

2. Data Processing & Analysis

2.1 Cell Segmentation

Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.

To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 1800], and the gene count per cell > 25. After filter the outliers, the qualified cells count is shown in the following table.

Outliers were filtered from the data, and the qualified cells count is presented in the following table. The identified cells after filtering are listed in the following table. In total, the study identified 219765 cells across 4 samples.

Segmented Cell Count in each Samples
Sample Index Cell Count
724GFP 64156
009GFP-cre 58084
011GFP 48946
008GFP-cre 48579
Identified Cell Spatial Overview on all Samples

Identified Cell Spatial Overview on all Samples

2.2 Batch Effect & Dimension Reduction

We use Scanpy for the analysis of single-cell level transcriptome data. The initial stage of our analysis involves the elimination of batch effects, thereby ensuring that different samples from various batches are distributed within the same domain and are statistically reasonable to be integrated and compared. To achieve this, we utilize the Harmony algorithm.

Subsequently, we present visualizations of the batch difference by Leiden UMAP clusters. Also, we illustrate the distributions of the Leiden clusters for future analysis.

Umap of cells and colored by batch

Umap of cells and colored by batch

Umap of cells on each batch

Umap of cells on each batch

Leiden Umap can be dividied to 28 clusters

Leiden Umap can be dividied to 28 clusters

2.3 Cell Annotation

We use a recent published tool: Map My Cell to perform cell type annotations for each cell. It is a high resolution cell type annotator build by Alan Institude, with nested levels of classification including 34 classes and 338 subclasses.

The taxonomy is based on the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3). Part of the used abbreviations is list in the supplementary Abbreviation. Otherwise can be found in CCFv3 paper.

With the annotation, we can identify and plot the selected types of cells in each sample.

2.3.1 Cell Annotation (Low resolution class)

MapMyCell Annotation Cell Count (Low resolution class)
class_name count
31 OPC-Oligo 44135
30 Astro-Epen 32941
01 IT-ET Glut 31657
33 Vascular 24933
09 CNU-LGE GABA 21244
34 Immune 13185
02 NP-CT-L6b Glut 7995
27 MY GABA 4783
29 CB Glut 4283
20 MB GABA 3398
18 TH Glut 3033
07 CTX-MGE GABA 2951
11 CNU-HYa GABA 2417
28 CB GABA 2314
24 MY Glut 2150
32 OEC 2132
12 HY GABA 2048
19 MB Glut 1999
06 CTX-CGE GABA 1950
23 P Glut 1926
13 CNU-HYa Glut 1647
26 P GABA 1640
10 LSX GABA 1258
08 CNU-MGE GABA 1253
05 OB-IMN GABA 1221
04 DG-IMN Glut 440
14 HY Glut 230
17 MH-LH Glut 154
03 OB-CR Glut 152
22 MB-HB Sero 109
21 MB Dopa 107
25 Pineal Glut 52
16 HY MM Glut 14
15 HY Gnrh1 Glut 14

2.3.2 Cell Annotation (High resolution subclass)

MapMyCell Annotation Cell Count (High resolution subclass)
subclass_name count
18 327 Oligo NN 40218
4 333 Endo NN 15499
19 319 Astro-TE NN 13267
27 062 STR D2 Gaba 12022
3 318 Astro-NT NN 9823
84 006 L4/5 IT CTX Glut 8720
46 334 Microglia NN 7514
10 321 Astroependymal NN 5968
284 061 STR D1 Gaba 5384
40 030 L6 CT CTX Glut 5189
1 314 CB Granule Glut 3952
44 326 OPC NN 3917
7 331 Peri NN 3837
24 004 L6 IT CTX Glut 3811
74 337 DC NN 3577
98 007 L2/3 IT CTX Glut 3208
6 330 VLMC NN 3104
107 063 STR D1 Sema5a Gaba 2909
268 151 TH Prkcd Grin2c Glut 2744
102 005 L5 IT CTX Glut 2711
99 009 L2/3 IT PIR-ENTl Glut 2600
35 017 CA3 Glut 2195
13 328 OEC NN 2132
38 338 Lymphoid NN 1820
12 332 SMC NN 1751
134 022 L5 ET CTX Glut 1664
42 306 SPVI-SPVC Sall3 Lhx1 Gly-Gaba 1604
83 052 Pvalb Gaba 1475
159 053 Sst Gaba 1244
8 311 CBX MLI Megf11 Gaba 1201
148 016 CA1-ProS Glut 1135
115 019 L2/3 IT PPP Glut 1090
156 012 MEA Slc17a7 Glut 960
116 029 L6b CTX Glut 953
58 285 MY Lhx1 Gly-Gaba 923
2 046 Vip Gaba 872
36 320 Astro-OLF NN 860
174 325 CHOR NN 857
91 181 IC Tfap2d Maf Glut 855
94 032 L5 NP CTX Glut 834
33 317 Astro-CB NN 796
86 198 IC Six3 En2 Gaba 765
172 093 RT-ZI Gnb3 Gaba 761
128 228 PSV Pvalb Lhx2 Glut 761
11 329 ABC NN 742
63 305 SPVI-SPVC Sall3 Nfib Gly-Gaba 681
29 101 ZI Pax6 Gaba 666
97 049 Lamp5 Gaba 649
252 113 MEA-COA-BMA Ccdc42 Glut 647
76 073 MEA-BST Sox6 Gaba 601
120 323 Ependymal NN 526
61 300 PARN-MDRNd-NTS Gbx2 Gly-Gaba 517
145 114 COAa-PAA-MEA Barhl2 Glut 512
20 041 OB-in Frmd7 Gaba 490
28 203 LGv-SPFp-SPFm Nkx2-2 Tcf7l2 Gaba 481
73 069 LSX Nkx2-1 Gaba 452
164 018 L2 IT PPP-APr Glut 446
219 168 SPA-SPFm-SPFp-POL-PIL-PoT Sp9 Glut 424
5 316 Bergmann NN 421
239 037 DG Glut 415
14 313 CBX Purkinje Gaba 410
194 014 LA-BLA-BMA-PA Glut 409
127 246 CU-ECU-SPVI Foxb1 Glut 403
54 322 Tanycyte NN 401
96 070 LSX Prdm12 Slit2 Gaba 399
65 256 SPVC Mafa Glut 398
100 010 IT AON-TT-DP Glut 395
166 064 STR-PAL Chst9 Gaba 375
195 002 IT EP-CLA Glut 369
23 315 DCO UBC Glut 331
143 278 NLL Gata3 Gly-Gaba 322
17 304 NTS-PARN Neurod2 Gly-Gaba 321
254 001 CLA-EPd-CTX Car3 Glut 314
298 060 OT D3 Folh1 Gaba 307
50 235 PG-TRN-LRN Fat2 Glut 305
153 057 NDB-SI-MA-STRv Lhx8 Gaba 305
123 279 PSV Pax2 Gly-Gaba 302
121 080 CEA-AAA-BST Six3 Sp9 Gaba 294
225 056 Sst Chodl Gaba 290
163 076 MEA-BST Lhx6 Nfib Gaba 285
53 222 PB Evx2 Glut 272
26 308 DCO Il22 Gly-Gaba 272
122 023 SUB-ProS Glut 269
224 013 COAp Grxcr2 Glut 257
117 027 L6b EPd Glut 256
15 054 STR Prox1 Lhx6 Gaba 253
68 201 PAG-RN Nkx2-2 Otx1 Gaba 253
9 312 CBX MLI Cdh22 Gaba 252
72 033 NP SUB Glut 250
52 028 L6b/CT ENT Glut 247
110 255 SPVO Mafa Meis2 Glut 246
87 197 SNr Six3 Gaba 242
25 047 Sncg Gaba 238
215 058 PAL-STR Gaba-Chol 238
106 254 VCO Mafa Meis2 Glut 234
113 210 PRT Mecom Gaba 228
237 026 NLOT Rho Glut 225
49 045 OB-STR-CTX Inh IMN 222
95 119 SI-MA-LPO-LHA Skor1 Glut 222
105 039 OB Meis2 Thsd7b Gaba 217
170 217 PB Lmx1a Glut 215
64 245 SPVI-SPVC Tlx3 Ebf3 Glut 213
162 003 L5/6 IT TPE-ENT Glut 207
69 243 PGRN-PARN-MDRN Hoxb5 Glut 207
226 074 MEA-BST Lhx6 Sp9 Gaba 204
59 025 CA2-FC-IG Glut 202
104 015 ENTmv-PA-COAp Glut 196
31 098 AHN-SBPV-PVHd Pdrm12 Gaba 193
119 048 RHP-COA Ndnf Gaba 191
157 202 PRT Tcf7l2 Gaba 187
34 335 BAM NN 186
193 082 CEA-BST Ebf1 Pdyn Gaba 177
71 199 PAG-MRN-RN Foxa2 Gaba 175
149 071 LSX Prdm12 Zeb2 Gaba 174
169 200 PAG-ND-PCG Onecut1 Gaba 173
290 055 STR Lhx8 Gaba 167
51 034 NP PPP Glut 165
178 265 PB Sst Gly-Gaba 161
109 153 MG-POL-SGN Nts Glut 160
125 195 SNr-VTA Pax5 Npas1 Gaba 145
150 182 CUN-PPN Evx2 Meis2 Glut 145
152 295 CBN Dmbx1 Gaba 145
229 090 BST-MPN Six3 Nrgn Gaba 144
88 277 DTN-LDT-IPN Otp Pax3 Gaba 142
210 036 HPF CR Glut 137
129 065 IA Mgp Gaba 133
158 263 CS-RPO Meis2 Gaba 127
16 043 OB-mi Frmd7 Gaba 124
89 270 LDT-DTN Gata3 Nfix Gaba 121
93 051 Pvalb chandelier Gaba 121
37 042 OB-out Frmd7 Gaba 114
285 079 CEA-BST Six3 Cyp26b1 Gaba 114
171 287 MV-SPIV-PRP Dmbx1 Gly-Gaba 114
276 059 GPe-SI Sox6 Cyp26b1 Gaba 114
62 257 SPVC Ccdc172 Glut 114
264 120 MEA Otp Foxp2 Glut 113
160 050 Lamp5 Lhx6 Gaba 111
155 216 MB-MY Tph2 Glut-Sero 109
137 215 SNc-VTA-RAmb Foxa1 Dopa 107
161 192 PPN-CUN-PCG Otp En1 Gaba 105
133 264 PRNc Otp Gly-Gaba 103
317 183 PBG Mtnr1a Glut-Chol 103
48 031 CT SUB Glut 101
184 283 PRP Otp Gly-Gaba 100
204 068 LSX Otx2 Gaba 96
101 072 LSX Sall3 Lmo1 Gaba 96
41 309 CB PLI Gly-Gaba 95
244 066 NDB-SI-ant Prdm12 Gaba 93
286 081 ACB-BST-FS D1 Gaba 90
243 104 TU-ARH Otp Six6 Gaba 90
257 075 MEA-BST Lhx6 Nr2e1 Gaba 89
138 336 Monocytes NN 88
167 196 PAG-PPN Pax5 Sox21 Gaba 84
22 310 CBX Golgi Gly-Gaba 84
67 085 SI-MPO-LPO Lhx8 Gaba 83
187 238 NTS Phox2b Glut 83
207 233 NLL-SOC Spp1 Glut 82
85 282 POR Spp1 Gly-Gaba 79
77 146 LH Pou4f1 Sox1 Glut 78
168 020 L2/3 IT RSP Glut 78
0 145 MH Tac2 Glut 76
246 088 BST Tac2 Gaba 73
66 258 SPVC Nmu Glut 72
142 224 PCG-PRNr Vsx2 Nkx6-1 Glut 69
130 267 CS-PRNr-PCG Tmem163 Otp Gaba 68
39 208 SC Lef1 Otx2 Gaba 68
82 213 SCsg Gabrr2 Gaba 66
151 008 L2/3 IT ENT Glut 64
135 290 MY Prox1 Lmo7 Gly-Gaba 64
205 162 CUN Evx2 Lhx2 Glut 63
111 089 PVR Six3 Sox3 Gaba 63
80 251 NTS Dbh Glut 58
177 221 LDT-PCG Vsx2 Lhx4 Glut 57
196 024 L5 PPP Glut 56
248 121 MEA-BST Otp Zic2 Glut 55
112 206 SCm-PAG Cdh23 Gaba 55
199 194 MRN-VTN-PPN Pax5 Cdh23 Gaba 54
176 134 PH-ant-LHA Otp Bsx Glut 54
30 293 PAS-MV Ebf2 Gly-Gaba 54
262 103 PVHd-DMH Lhx6 Gaba 53
55 147 AD Serpinb7 Glut 52
47 262 Pineal Crx Glut 52
186 109 LGv-ZI Otx2 Gaba 51
118 011 L2 IT ENT-po Glut 51
190 271 NI-RPO Gata3 Nr4a2 Gaba 51
220 209 SCs Pax7 Nfia Gaba 47
206 205 SC-PAG Lef1 Emx2 Gaba 45
57 044 OB Dopa-Gaba 45
140 297 CU-ECU Pax2 Gly-Gaba 45
263 218 PSV Lmx1a Trpv6 Glut 44
108 214 IPN Otp Crisp1 Gaba 42
154 268 CS-PRNr-DR En1 Sox2 Gaba 42
136 169 PAG-SC Pou4f1 Zic1 Glut 41
45 067 LSX Sall3 Pax6 Gaba 41
218 207 SCs Dmbx1 Gaba 40
234 100 AHN Onecut3 Gaba 40
245 299 MARN-PPY Ngfr Gly-Gaba 39
81 276 LDT-PCG St18 Gaba 38
90 204 SC Otx2 Gcnt4 Gaba 34
114 172 PAG Pou4f1 Ebf2 Glut 33
201 154 PF Fzd5 Glut 33
180 212 SCs Lef1 Gli3 Gaba 32
266 107 DMH Hmx2 Gaba 32
208 086 MPO-ADP Lhx8 Gaba 32
202 083 CEA-BST Rai14 Pdyn Crh Gaba 32
203 141 PH-SUM Foxa1 Glut 32
175 193 MRN-PPN-CUN Pax8 Gaba 31
211 170 PAG-MRN Tfap2b Glut 30
213 288 MDRN Hoxb5 Ebf2 Gly-Gaba 29
200 174 PAG Pou4f2 Mesi2 Glut 29
131 211 SC Tnnt1 Gli3 Gaba 29
278 108 ARH-PVp Tbx3 Gaba 28
249 115 MS-SF Bsx Glut 27
43 275 PDTg Otp Olig3 Gaba 27
181 102 DMH-LHA Gsx1 Gaba 27
212 180 SCiw Pitx2 Glut 26
240 234 MEV Ppp1r1c Glut 26
189 250 CBN Neurod2 Pvalb Glut 26
141 286 PPY-PGRNl Vip Glyc-Gaba 26
288 106 PVpo-VMPO-MPN Hmx2 Gaba 25
21 021 L4 RSP-ACA Glut 25
78 038 DG-PIR Ex IMN 25
126 261 HB Calcb Chol 25
60 229 PB-NTS Phox2b Ebf3 Lmx1b Glut 24
214 248 MV-SPIV Zic4 Neurod2 Glut 24
183 133 PVH-SO-PVa Otp Glut 24
92 303 IRN Dmbx1 Pax2 Gly-Gaba 24
227 177 SCig-an-PPT Foxb1 Glut 24
231 160 PAG-SC Neurod2 Meis2 Glut 24
232 226 PRNc-PARN Tlx1 Glut 24
173 124 MPN-MPO-PVpo Hmx2 Glut 24
287 135 STN-PSTN Pitx2 Glut 24
147 324 Hypendymal NN 22
241 129 VMH Nr5a1 Glut 21
269 149 PVT-PT Ntrk1 Glut 21
260 273 PDTg-PCG Pax6 Gaba 21
228 173 PAG Pou4f2 Glut 21
293 112 GPi Tbr1 Cngb3 Gaba-Glut 21
146 187 SCsg Pde5a Glut 20
256 105 TMd-DMH Foxd2 Gaba 19
292 272 LDT-PCG-CS Gata3 Lhx1 Gaba 18
70 132 AHN-RCH-LHA Otp Fezf1 Glut 17
308 122 LHA-MEA Otp Glut 17
32 302 MV Xdh Gly-Gaba 17
75 191 PAG-MRN Rln3 Gaba 17
182 167 PRC-PAG Tcf7l2 Irx2 Glut 17
259 094 SCH Six6 Cdc14a Gaba 16
103 225 PRNc-NI-SG-RPO Vsx2 Nr4a2 Glut 16
216 188 SCop Sln Glut 16
139 231 IPN-LDT Vsx2 Nkx6-1 Glut 16
165 291 NTS-MDRNd Prox1 Zic1 Gly-Gaba 16
291 099 SBPV-PVa Six6 Satb2 Gaba 15
282 087 MPN-MPO-LPO Lhx6 Zfhx3 Gaba 15
255 035 OB Eomes Ms4a15 Glut 15
271 097 PVHd-SBPV Six3 Prox1 Gaba 15
280 284 GRN-IRN-MDRNd Ikzf1 Gly-Gaba 14
265 296 RPA Pax6 Hoxb5 Gly-Gaba 14
275 152 RE-Xi Nox4 Glut 14
209 142 HY Gnrh1 Glut 14
198 247 MV-SPIV Phox2b Ebf3 Lbx1 Glut 14
222 298 PRP Gata3 Slc6a5 Gly-Gaba 13
79 111 TRS-BAC Sln Glut 13
267 155 PRC-PAG Pax6 Glut 13
192 176 SCig Foxb1 Glut 13
185 144 MM Foxb1 Glut 12
132 178 SCig Foxb1 Otx2 Glut 12
188 281 POR Gata3 Gly-Gaba 11
221 171 PAG Pou4f1 Bnc2 Glut 11
217 237 PRP-NI-PRNc-GRN Otp Glut 11
302 078 SI-MA-ACB Ebf1 Bnc2 Gaba 11
301 232 LDT Vsx2 Nkx6-1 Nfib Glut 10
296 084 BST-SI-AAA Six3 Slc22a3 Gaba 10
247 227 PB-PSV Phox2b Glut 10
235 220 PB Pax5 Glut 9
258 117 LHA Barhl2 Glut 9
197 223 B-PB Nr4a2 Glut 9
299 040 OB Trdn Gaba 9
289 307 RO-RPA Pkd2l1 Gaba 9
233 165 PAG-MRN Pou3f1 Glut 9
273 244 MV-SPIV Slc6a2 Glut 8
179 175 SC Bnc2 Glut 8
144 140 PMd-LHA Foxb1 Glut 8
303 077 CEA-BST Gal Avp Gaba 7
272 252 DMX VII Tbx20 Chol 7
253 159 IF-RL-CLI-PAG Foxa1 Glut 7
251 301 MV Nr4a2 Gly-Gaba 6
283 091 ARH-PVi Six6 Dopa-Gaba 6
238 123 DMH Nkx2-4 Glut 6
316 294 MV Pax6 Gly-Gaba 6
300 161 PAG Pou4f3 Glut 6
261 128 VMH Fezf1 Glut 6
294 092 TMv-PMv Tbx3 Hist-Gaba 6
191 136 PMv-TMv Pitx2 Glut 5
223 156 MB-ant-ve Dmrta2 Glut 5
274 148 AV Col27a1 Glut 5
277 150 CM-IAD-CL-PCN Sema5b Glut 4
315 118 ADP-MPO Trp73 Glut 4
279 269 LDT Fgf7 Gaba 4
56 190 ND-INC Foxd2 Glut 4
321 116 AVPV-MEPO-SFO Tbr1 Glut 4
295 236 IRN Vip Glut 3
297 096 PVHd Gsc Gaba 3
270 164 APN C1ql4 Glut 3
314 157 RN Spp1 Glut 3
313 166 MRN Pou3f1 C1ql4 Glut 3
306 110 BST-po Iigp1 Glut 3
307 139 PH-LHA Foxb1 Glut 3
311 230 PRNr Otp Nfib Glut 2
318 280 NLL-po Pax7 Gaba 2
312 143 MM-ant Foxb1 Glut 2
242 126 ARH-PVp Tbx3 Glut 2
310 138 PH Pitx2 Glut 2
305 095 DMH Prdm13 Gaba 2
124 185 SCig Tfap2b Chrnb3 Glut 2
230 186 SCop Pou4f2 Neurod2 Glut 2
250 260 MDRNv Crp Glut 2
309 189 PAG Ucn Glut 1
304 239 MARN-GRN Pyy Glut 1
281 292 MV Nkx6-1 Gly-Gaba 1
319 249 NTS Aldh1a2 Glut 1
320 289 MDRNd Prox1 Pax6 Gly-Gaba 1
236 130 LHA Pmch Glut 1
322 274 PDTg Otp Shroom3 Gaba 1
323 137 PH-an Pitx2 Glut 1
324 219 PB-SUT Tlx3 Lhx2 Glut 1

2.3.3 Spatial cell type (Neurons)

2.3.4 Spatial cell type (Non-Neurons)

3. Gene differentiation

3.1 koGFP v.s. GFPcre

Here, we use Wilcoxon rank-sum to compute differential expression.

The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.

Cell amount compare: ‘GFP-cre’: 113102, ‘GFP’: 106663.

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
18 App 44.736282 5.972642 0 0
10 Plp1 49.036137 5.718488 0 0
499 Cd74 -59.552753 -4.692116 0 0
9 Syp 50.261590 3.794836 0 0
5 Cx3cl1 51.666542 2.978154 0 0
14 Nr4a1 45.554310 2.809042 0 0
35 Dnm1 36.316257 2.760810 0 0
492 C3 -17.730808 -2.572384 0 0
495 Serpina3n -24.721464 -2.536104 0 0
76 Cldn11 26.102417 2.483486 0 0
12 Arc 47.141872 2.393958 0 0
22 Egr1 42.227780 2.354570 0 0
496 C4b -37.432564 -2.293783 0 0
481 Itgal -10.370717 -2.274252 0 0
497 Ctss -44.824154 -2.194577 0 0
13 Hpca 45.568264 2.185736 0 0
7 Camk2a 51.449840 2.146260 0 0
475 Cxcl10 -8.422120 -2.045975 0 0
19 Eno2 44.523117 2.018411 0 0
15 Bcan 45.452614 1.913053 0 0
2 Rph3a 57.176254 1.886615 0 0
491 Ly9 -17.487762 -1.883386 0 0
23 Gria2 42.109333 1.831859 0 0
486 Clec7a -12.054828 -1.825047 0 0
39 Bsg 34.559450 1.807745 0 0
29 Syngap1 38.492718 1.746275 0 0
0 Cspg5 72.560670 1.717004 0 0
17 Grin2b 45.100048 1.701919 0 0
4 Fam131a 53.949270 1.689317 0 0
97 Apoe 19.690727 -1.685822 0 0
31 Gria1 37.508610 1.675839 0 0
68 Egr4 26.828337 1.653498 0 0
8 Bin1 50.626930 1.589708 0 0
487 Cst7 -12.510269 -1.582236 0 0
480 Lgals3 -9.810495 -1.578655 0 0
27 Cplx1 39.918278 1.556089 0 0
114 Egr2 16.973430 1.551940 0 0
60 Fos 29.335768 1.530916 0 0
498 Gfap -59.169655 -1.496276 0 0
24 Dlg4 41.551414 1.495855 0 0
74 Olig1 26.309402 1.414519 0 0
25 Enpp2 40.683018 1.389329 0 0
72 Grin1 26.615938 1.379400 0 0
26 Adrb1 40.252403 1.307181 0 0
150 Fosb 13.704445 1.267708 0 0
30 Grin2a 38.490376 1.260622 0 0
102 Slc17a7 18.938023 1.256663 0 0
494 C1qa -22.363613 -1.247561 0 0
36 Nefm 35.932125 1.214934 0 0
3 Sox8 56.846880 1.198911 0 0
81 Fosl2 24.503006 1.174972 0 0
6 Pcdh9 51.520077 1.172719 0 0
58 Mog 29.780993 1.172717 0 0
16 Mapt 45.247490 1.171918 0 0
47 Kcnc1 32.310510 1.171672 0 0
38 Grm4 34.620040 1.070396 0 0
163 Otof 12.611641 1.066515 0 0
41 Syn1 34.270800 1.046408 0 0
108 Nr4a2 18.551891 1.038631 0 0
48 Nptxr 32.190388 1.007296 0 0

3.2 Microglia (GFP-cre v.s. GFP)

Here, we use Wilcoxon rank-sum to compute differential expression in Microglia cells.

The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.

Cell number: ‘GFP’: 4408, ‘GFP-cre’: 3106.

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
490 Apoe -13.160284 -22.351469 0.0000000 0.0000000
499 Cd74 -38.976810 -13.935299 0.0000000 0.0000000
0 Cx3cr1 26.206287 7.033817 0.0000000 0.0000000
498 C4b -26.623106 -6.578667 0.0000000 0.0000000
2 Selplg 20.464607 6.321182 0.0000000 0.0000000
497 Ctss -19.661251 -6.129716 0.0000000 0.0000000
494 C3 -15.745511 -5.026065 0.0000000 0.0000000
492 Cst7 -14.186185 -4.969236 0.0000000 0.0000000
1 Tmem119 23.285162 4.661632 0.0000000 0.0000000
482 Lgals3 -8.555458 -4.631769 0.0000000 0.0000000
8 Csf1r 11.874363 4.079345 0.0000000 0.0000000
460 Cxcl10 -3.207307 -3.755650 0.0013398 0.0066992
486 Spp1 -9.400478 -3.616108 0.0000000 0.0000000
480 Itgal -8.187654 -3.544304 0.0000000 0.0000000
493 Itgax -14.559648 -3.468330 0.0000000 0.0000000
463 Serpina3n -3.701132 -3.420096 0.0002146 0.0011665
479 Clec7a -7.250827 -3.344504 0.0000000 0.0000000
495 Csf1 -16.713840 -3.097090 0.0000000 0.0000000
481 Cxcl2 -8.319359 -3.043944 0.0000000 0.0000000
484 Xdh -9.306241 -2.891892 0.0000000 0.0000000
489 Ctsb -12.294172 -2.877592 0.0000000 0.0000000
488 Gpc3 -9.518273 -2.734765 0.0000000 0.0000000
453 Cd8a -2.680199 -2.181966 0.0073578 0.0309153
465 Fmo1 -3.818512 -2.171021 0.0001343 0.0007543
496 Gfap -17.119291 -2.134081 0.0000000 0.0000000
491 Ly9 -13.968450 -1.968051 0.0000000 0.0000000
485 Rgs12 -9.392124 -1.915597 0.0000000 0.0000000
487 Ddit3 -9.515569 -1.732437 0.0000000 0.0000000
461 Neu4 -3.387595 -1.702926 0.0007051 0.0036723
462 Tnf -3.400176 -1.643806 0.0006734 0.0035443
483 Cd83 -8.730924 -1.618328 0.0000000 0.0000000
4 Camk2a 13.917956 1.606004 0.0000000 0.0000000
6 Syp 13.472908 1.558124 0.0000000 0.0000000
11 Hpca 10.603275 1.402991 0.0000000 0.0000000
9 Rph3a 11.841915 1.400866 0.0000000 0.0000000
26 Cspg5 7.203558 1.310284 0.0000000 0.0000000
466 Kit -4.009469 -1.295562 0.0000609 0.0003580
458 Rspo1 -3.157602 -1.279444 0.0015907 0.0077977
18 Bcan 8.361877 1.263355 0.0000000 0.0000000
470 Atf3 -4.577908 -1.232095 0.0000047 0.0000305
3 Siglech 14.975441 1.175270 0.0000000 0.0000000
48 Nr4a1 4.486057 1.162832 0.0000073 0.0000459
5 P2ry12 13.843489 1.154090 0.0000000 0.0000000
13 Dnm1 9.099365 1.148387 0.0000000 0.0000000
455 Egr2 -2.822682 -1.144313 0.0047624 0.0212606
41 App 4.928330 1.136704 0.0000008 0.0000060
477 Itpr2 -6.039866 -1.116609 0.0000000 0.0000000
20 Fam131a 8.053680 1.078608 0.0000000 0.0000000
473 Bcl11b -4.971124 -1.075480 0.0000007 0.0000050
12 Eno2 10.375032 1.073601 0.0000000 0.0000000
37 Cx3cl1 5.368049 1.068547 0.0000001 0.0000006
478 Bcl6 -6.933073 -1.058754 0.0000000 0.0000000
69 Neto1 2.708440 1.054087 0.0067600 0.0291381
7 Dlg4 12.360530 1.042307 0.0000000 0.0000000
29 Arc 6.311123 1.030949 0.0000000 0.0000000

3.3 Endothelia cells (GFP-cre v.s. GFP)

Here, we use Wilcoxon rank-sum to compute differential expression in Endothelia cells.

The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.

Cell number: ‘GFP-cre’: 8497, ‘GFP’: 7002.

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
4 Bsg 17.046259 7.096224 0.0000000 0.0000000
1 Cldn5 19.304459 4.063761 0.0000000 0.0000000
498 Cd74 -8.365247 -2.673357 0.0000000 0.0000000
0 Flt1 23.034956 2.247791 0.0000000 0.0000000
21 Nr4a1 7.165558 2.043065 0.0000000 0.0000000
5 Apoe 15.964951 1.785722 0.0000000 0.0000000
9 App 11.192018 1.747558 0.0000000 0.0000000
499 Gfap -14.007896 -1.482300 0.0000000 0.0000000
59 Fos 4.055646 1.470903 0.0000500 0.0003846
493 C4b -3.615977 -1.387801 0.0002992 0.0021072
28 Egr1 6.308252 1.109528 0.0000000 0.0000000
494 Ctss -3.975957 -1.091061 0.0000701 0.0005231
12 Synpo2 10.440583 1.074914 0.0000000 0.0000000
2 Ctnnb1 18.271220 1.005527 0.0000000 0.0000000

3.4 CA1 (GFP-cre v.s. GFP)

Here, we use Wilcoxon rank-sum to compute differential expression in CA1 cells.

The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.

Cell number: ‘GFP-cre’: 862, ‘GFP’: 273.

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
0 Hpca 13.111697 20.114042 0.0000000 0.0000000
22 Gria1 7.589025 15.772917 0.0000000 0.0000000
495 Nptxr -10.765465 -15.584857 0.0000000 0.0000000
1 Fam131a 11.959662 11.401796 0.0000000 0.0000000
4 Grin2a 11.653724 11.238268 0.0000000 0.0000000
2 Ptk2b 11.802985 11.177084 0.0000000 0.0000000
10 Camk2a 10.252531 11.152108 0.0000000 0.0000000
499 Col6a1 -12.229265 -11.023427 0.0000000 0.0000000
12 Dkk3 10.181343 9.752980 0.0000000 0.0000000
5 Arc 11.546942 9.558531 0.0000000 0.0000000
15 Nr4a1 8.905788 9.050091 0.0000000 0.0000000
7 Wfs1 11.329247 7.839121 0.0000000 0.0000000
65 App 3.202817 7.816557 0.0013609 0.0075606
11 Egr1 10.182191 7.584926 0.0000000 0.0000000
14 Cx3cl1 9.515970 7.312509 0.0000000 0.0000000
23 Grin2b 7.548241 7.112894 0.0000000 0.0000000
32 Gria2 5.897891 6.622412 0.0000000 0.0000000
29 Cpne6 6.761891 6.337827 0.0000000 0.0000000
39 Grin1 5.297138 6.221646 0.0000001 0.0000011
3 Kcnab1 11.668873 6.177465 0.0000000 0.0000000
40 Syp 5.153067 6.095230 0.0000003 0.0000024
6 Bcan 11.405944 5.269656 0.0000000 0.0000000
8 Gm2115 11.292594 5.015296 0.0000000 0.0000000
47 Syngap1 4.830179 4.747772 0.0000014 0.0000110
497 Nr2f2 -11.678724 -4.695108 0.0000000 0.0000000
498 Nnat -12.216023 -4.622992 0.0000000 0.0000000
69 Dnm1 2.954613 4.499082 0.0031306 0.0161372
493 Crtac1 -9.447854 -4.447514 0.0000000 0.0000000
491 Grp -8.558642 -4.210013 0.0000000 0.0000000
45 Eno2 4.954228 4.128691 0.0000007 0.0000061
494 Adgra1 -10.327109 -3.981628 0.0000000 0.0000000
479 Cd74 -3.730581 -3.966161 0.0001910 0.0011508
478 Nptx1 -3.711302 -3.910166 0.0002062 0.0012274
496 Plagl1 -11.552451 -3.754816 0.0000000 0.0000000
20 Itga7 7.788182 3.707352 0.0000000 0.0000000
21 Egr4 7.634048 3.522362 0.0000000 0.0000000
9 Epha7 11.154562 3.462725 0.0000000 0.0000000
489 Hrh3 -7.111580 -3.399637 0.0000000 0.0000000
481 Oxtr -3.924017 -3.322877 0.0000871 0.0005443
24 Rbfox3 7.177471 3.254410 0.0000000 0.0000000
488 Trib2 -5.944926 -3.246603 0.0000000 0.0000000
28 Epha10 6.863376 3.198907 0.0000000 0.0000000
36 Lct 5.597991 3.186000 0.0000000 0.0000002
492 Gfap -9.152086 -3.083316 0.0000000 0.0000000
17 Kcnd2 8.110752 2.968716 0.0000000 0.0000000
16 Neurod6 8.615953 2.950619 0.0000000 0.0000000
25 Kcnh7 7.124398 2.666600 0.0000000 0.0000000
60 Dlg4 4.006752 2.657844 0.0000616 0.0003946
490 Nos1 -7.155966 -2.643271 0.0000000 0.0000000
480 Ly6g6e -3.764269 -2.631040 0.0001670 0.0010311
18 Nr4a2 7.983525 2.622531 0.0000000 0.0000000
462 Ctss -2.671133 -2.616871 0.0075596 0.0343617
464 Otof -2.732151 -2.566950 0.0062922 0.0291307
54 Lratd2 4.322436 2.529932 0.0000154 0.0001087
35 Gpr63 5.660386 2.527436 0.0000000 0.0000002
44 Brinp1 5.045332 2.523550 0.0000005 0.0000038
13 Nefm 10.026256 2.517317 0.0000000 0.0000000
52 Zbtb20 4.493308 2.417756 0.0000070 0.0000508
27 Cck 6.973759 2.368450 0.0000000 0.0000000
58 Col11a1 4.087050 2.331447 0.0000437 0.0002874
460 Mfsd2a -2.636598 -2.330735 0.0083742 0.0373848
33 Drd5 5.788672 2.164355 0.0000000 0.0000001
26 Gabra1 6.996853 2.135416 0.0000000 0.0000000
472 Myh11 -2.939464 -1.960730 0.0032878 0.0167745
34 Scn4b 5.688247 1.931303 0.0000000 0.0000001
470 Npy -2.914146 -1.931014 0.0035666 0.0178332
19 Bcl6 7.972931 1.893637 0.0000000 0.0000000
62 Wnt2 3.601977 1.877229 0.0003158 0.0018577
59 Fos 4.041393 1.874660 0.0000531 0.0003450
48 Sorl1 4.787488 1.810903 0.0000017 0.0000134
56 Meis2 4.131754 1.765681 0.0000360 0.0002432
63 Gria3 3.438203 1.668010 0.0005856 0.0033655
476 Grin3a -3.237775 -1.643861 0.0012047 0.0067677
38 Lmo1 5.439196 1.643091 0.0000001 0.0000005
31 Pkp2 6.021940 1.642286 0.0000000 0.0000000
477 Deptor -3.480153 -1.526833 0.0005011 0.0029135
61 Adgrl2 3.754840 1.520386 0.0001735 0.0010576
41 Crhr1 5.131668 1.517439 0.0000003 0.0000026
55 Plekhg1 4.233664 1.514918 0.0000230 0.0001597
70 Hs3st1 2.847513 1.484375 0.0044062 0.0213894
46 Htr1a 4.897871 1.425808 0.0000010 0.0000079
30 Bcl11b 6.415380 1.420154 0.0000000 0.0000000
484 Fam107a -4.499664 -1.401763 0.0000068 0.0000507
72 Bin1 2.598250 1.345265 0.0093700 0.0414603
37 Ctsb 5.486760 1.334361 0.0000000 0.0000004
50 Adrb1 4.590556 1.333000 0.0000044 0.0000340
485 Tpbg -4.566297 -1.305343 0.0000050 0.0000376
461 Lrrc55 -2.646450 -1.292745 0.0081342 0.0366403
465 Bsg -2.739037 -1.287415 0.0061620 0.0287942
67 Car4 3.034381 1.261995 0.0024103 0.0126858
487 Tcerg1l -5.172665 -1.253383 0.0000002 0.0000022
483 Cnr1 -4.227625 -1.239971 0.0000236 0.0001618
469 Tacr3 -2.900692 -1.232076 0.0037234 0.0184326
71 Ndst4 2.795288 1.222578 0.0051854 0.0246922
49 Smad3 4.750517 1.199729 0.0000020 0.0000159
53 Robo1 4.462269 1.194761 0.0000081 0.0000579
57 Npy2r 4.110038 1.188083 0.0000396 0.0002637
43 Fibcd1 5.052112 -1.187138 0.0000004 0.0000038
466 Ccl6 -2.757681 -1.085428 0.0058213 0.0274589
473 Igfbp6 -3.081628 -1.022652 0.0020587 0.0109506

4. Hippocampal Region

4.1 Hippocampal Region Selection

Cell Selection Count in Hippocampal Region
Counts
724GFP 5430
011GFP 3695
009GFP-cre 2495
008GFP-cre 4294

4.2 Cell Types in Hippo

Cell Type Count in Hippocampal Region
subclass_name count
2 327 Oligo NN 2011
92 337 DC NN 1445
127 062 STR D2 Gaba 1272
3 319 Astro-TE NN 1159
14 334 Microglia NN 1104
4 333 Endo NN 963
79 017 CA3 Glut 747
64 016 CA1-ProS Glut 745
6 321 Astroependymal NN 492
90 009 L2/3 IT PIR-ENTl Glut 440
61 338 Lymphoid NN 431
0 318 Astro-NT NN 408
8 326 OPC NN 336
1 331 Peri NN 271
155 061 STR D1 Gaba 257
63 037 DG Glut 245
154 063 STR D1 Sema5a Gaba 185
46 330 VLMC NN 180
5 328 OEC NN 134
74 025 CA2-FC-IG Glut 129
42 010 IT AON-TT-DP Glut 120
29 332 SMC NN 96
249 026 NLOT Rho Glut 87
215 114 COAa-PAA-MEA Barhl2 Glut 79
174 057 NDB-SI-MA-STRv Lhx8 Gaba 72
238 120 MEA Otp Foxp2 Glut 70
73 023 SUB-ProS Glut 67
150 073 MEA-BST Sox6 Gaba 63
7 285 MY Lhx1 Gly-Gaba 61
57 119 SI-MA-LPO-LHA Skor1 Glut 56
140 007 L2/3 IT CTX Glut 53
70 030 L6 CT CTX Glut 52
20 306 SPVI-SPVC Sall3 Lhx1 Gly-Gaba 50
34 006 L4/5 IT CTX Glut 49
100 012 MEA Slc17a7 Glut 49
144 335 BAM NN 48
82 320 Astro-OLF NN 47
172 060 OT D3 Folh1 Gaba 45
112 013 COAp Grxcr2 Glut 43
71 028 L6b/CT ENT Glut 42
69 069 LSX Nkx2-1 Gaba 36
72 046 Vip Gaba 36
27 329 ABC NN 34
85 064 STR-PAL Chst9 Gaba 34
68 049 Lamp5 Gaba 34
32 052 Pvalb Gaba 34
94 304 NTS-PARN Neurod2 Gly-Gaba 33
134 048 RHP-COA Ndnf Gaba 32
80 058 PAL-STR Gaba-Chol 32
108 019 L2/3 IT PPP Glut 32
116 004 L6 IT CTX Glut 32
170 056 Sst Chodl Gaba 31
171 080 CEA-AAA-BST Six3 Sp9 Gaba 30
106 070 LSX Prdm12 Slit2 Gaba 29
62 033 NP SUB Glut 26
101 050 Lamp5 Lhx6 Gaba 26
24 300 PARN-MDRNd-NTS Gbx2 Gly-Gaba 25
44 317 Astro-CB NN 24
110 036 HPF CR Glut 23
148 001 CLA-EPd-CTX Car3 Glut 22
65 027 L6b EPd Glut 22
137 047 Sncg Gaba 22
13 305 SPVI-SPVC Sall3 Nfib Gly-Gaba 21
216 085 SI-MPO-LPO Lhx8 Gaba 21
213 074 MEA-BST Lhx6 Sp9 Gaba 20
67 029 L6b CTX Glut 19
241 113 MEA-COA-BMA Ccdc42 Glut 19
109 053 Sst Gaba 19
9 255 SPVO Mafa Meis2 Glut 19
28 243 PGRN-PARN-MDRN Hoxb5 Glut 19
49 322 Tanycyte NN 19
19 279 PSV Pax2 Gly-Gaba 18
135 041 OB-in Frmd7 Gaba 17
159 336 Monocytes NN 17
132 005 L5 IT CTX Glut 16
133 054 STR Prox1 Lhx6 Gaba 16
102 045 OB-STR-CTX Inh IMN 16
12 101 ZI Pax6 Gaba 15
11 278 NLL Gata3 Gly-Gaba 15
15 254 VCO Mafa Meis2 Glut 15
48 216 MB-MY Tph2 Glut-Sero 14
146 032 L5 NP CTX Glut 14
115 014 LA-BLA-BMA-PA Glut 14
125 039 OB Meis2 Thsd7b Gaba 14
158 199 PAG-MRN-RN Foxa2 Gaba 13
149 200 PAG-ND-PCG Onecut1 Gaba 13
45 222 PB Evx2 Glut 13
66 031 CT SUB Glut 13
30 210 PRT Mecom Gaba 13
220 098 AHN-SBPV-PVHd Pdrm12 Gaba 13
33 201 PAG-RN Nkx2-2 Otx1 Gaba 11
95 323 Ependymal NN 11
166 066 NDB-SI-ant Prdm12 Gaba 11
114 015 ENTmv-PA-COAp Glut 11
105 315 DCO UBC Glut 11
38 228 PSV Pvalb Lhx2 Glut 10
103 072 LSX Sall3 Lmo1 Gaba 10
31 022 L5 ET CTX Glut 10
214 065 IA Mgp Gaba 9
25 246 CU-ECU-SPVI Foxb1 Glut 9
23 264 PRNc Otp Gly-Gaba 9
218 059 GPe-SI Sox6 Cyp26b1 Gaba 9
161 055 STR Lhx8 Gaba 9
223 088 BST Tac2 Gaba 9
195 051 Pvalb chandelier Gaba 9
17 235 PG-TRN-LRN Fat2 Glut 9
145 034 NP PPP Glut 8
10 020 L2/3 IT RSP Glut 8
47 217 PB Lmx1a Glut 8
210 203 LGv-SPFp-SPFm Nkx2-2 Tcf7l2 Gaba 8
167 198 IC Six3 En2 Gaba 8
189 188 SCop Sln Glut 8
16 181 IC Tfap2d Maf Glut 8
239 075 MEA-BST Lhx6 Nr2e1 Gaba 8
190 090 BST-MPN Six3 Nrgn Gaba 8
36 277 DTN-LDT-IPN Otp Pax3 Gaba 7
35 224 PCG-PRNr Vsx2 Nkx6-1 Glut 7
201 151 TH Prkcd Grin2c Glut 7
185 003 L5/6 IT TPE-ENT Glut 7
168 079 CEA-BST Six3 Cyp26b1 Gaba 7
153 082 CEA-BST Ebf1 Pdyn Gaba 6
129 089 PVR Six3 Sox3 Gaba 6
26 282 POR Spp1 Gly-Gaba 6
208 038 DG-PIR Ex IMN 6
182 081 ACB-BST-FS D1 Gaba 6
200 195 SNr-VTA Pax5 Npas1 Gaba 6
151 071 LSX Prdm12 Zeb2 Gaba 6
221 202 PRT Tcf7l2 Gaba 6
217 078 SI-MA-ACB Ebf1 Bnc2 Gaba 6
97 263 CS-RPO Meis2 Gaba 6
123 265 PB Sst Gly-Gaba 6
75 002 IT EP-CLA Glut 6
93 093 RT-ZI Gnb3 Gaba 6
118 011 L2 IT ENT-po Glut 6
58 316 Bergmann NN 6
107 271 NI-RPO Gata3 Nr4a2 Gaba 5
89 308 DCO Il22 Gly-Gaba 5
226 084 BST-SI-AAA Six3 Slc22a3 Gaba 5
87 134 PH-ant-LHA Otp Bsx Glut 5
113 314 CB Granule Glut 5
41 238 NTS Phox2b Glut 5
121 283 PRP Otp Gly-Gaba 5
160 068 LSX Otx2 Gaba 5
22 297 CU-ECU Pax2 Gly-Gaba 5
78 209 SCs Pax7 Nfia Gaba 4
83 115 MS-SF Bsx Glut 4
152 008 L2/3 IT ENT Glut 4
56 261 HB Calcb Chol 4
99 182 CUN-PPN Evx2 Meis2 Glut 4
184 324 Hypendymal NN 4
77 121 MEA-BST Otp Zic2 Glut 4
117 018 L2 IT PPP-APr Glut 4
186 024 L5 PPP Glut 4
142 251 NTS Dbh Glut 4
177 108 ARH-PVp Tbx3 Gaba 4
179 270 LDT-DTN Gata3 Nfix Gaba 4
227 086 MPO-ADP Lhx8 Gaba 3
43 141 PH-SUM Foxa1 Glut 3
209 083 CEA-BST Rai14 Pdyn Crh Gaba 3
176 207 SCs Dmbx1 Gaba 3
207 102 DMH-LHA Gsx1 Gaba 3
191 123 DMH Nkx2-4 Glut 3
173 040 OB Trdn Gaba 3
98 205 SC-PAG Lef1 Emx2 Gaba 3
141 234 MEV Ppp1r1c Glut 3
131 287 MV-SPIV-PRP Dmbx1 Gly-Gaba 3
199 196 PAG-PPN Pax5 Sox21 Gaba 3
59 142 HY Gnrh1 Glut 3
52 162 CUN Evx2 Lhx2 Glut 3
197 325 CHOR NN 3
139 168 SPA-SPFm-SPFp-POL-PIL-PoT Sp9 Glut 3
156 214 IPN Otp Crisp1 Gaba 3
21 221 LDT-PCG Vsx2 Lhx4 Glut 3
240 215 SNc-VTA-RAmb Foxa1 Dopa 3
40 229 PB-NTS Phox2b Ebf3 Lmx1b Glut 3
183 232 LDT Vsx2 Nkx6-1 Nfib Glut 3
157 147 AD Serpinb7 Glut 3
246 106 PVpo-VMPO-MPN Hmx2 Gaba 2
50 267 CS-PRNr-PCG Tmem163 Otp Gaba 2
203 104 TU-ARH Otp Six6 Gaba 2
193 172 PAG Pou4f1 Ebf2 Glut 2
76 293 PAS-MV Ebf2 Gly-Gaba 2
196 124 MPN-MPO-PVpo Hmx2 Glut 2
165 313 CBX Purkinje Gaba 2
206 136 PMv-TMv Pitx2 Glut 2
55 109 LGv-ZI Otx2 Gaba 2
124 208 SC Lef1 Otx2 Gaba 2
136 194 MRN-VTN-PPN Pax5 Cdh23 Gaba 2
237 116 AVPV-MEPO-SFO Tbr1 Glut 2
60 256 SPVC Mafa Glut 2
37 176 SCig Foxb1 Glut 2
147 192 PPN-CUN-PCG Otp En1 Gaba 2
162 094 SCH Six6 Cdc14a Gaba 2
180 275 PDTg Otp Olig3 Gaba 2
212 092 TMv-PMv Tbx3 Hist-Gaba 2
169 206 SCm-PAG Cdh23 Gaba 2
242 103 PVHd-DMH Lhx6 Gaba 2
130 299 MARN-PPY Ngfr Gly-Gaba 2
219 193 MRN-PPN-CUN Pax8 Gaba 1
247 169 PAG-SC Pou4f1 Zic1 Glut 1
222 268 CS-PRNr-DR En1 Sox2 Gaba 1
235 273 PDTg-PCG Pax6 Gaba 1
248 097 PVHd-SBPV Six3 Prox1 Gaba 1
224 274 PDTg Otp Shroom3 Gaba 1
225 100 AHN Onecut3 Gaba 1
245 140 PMd-LHA Foxb1 Glut 1
244 122 LHA-MEA Otp Glut 1
228 118 ADP-MPO Trp73 Glut 1
229 157 RN Spp1 Glut 1
230 067 LSX Sall3 Pax6 Gaba 1
243 191 PAG-MRN Rln3 Gaba 1
231 174 PAG Pou4f2 Mesi2 Glut 1
232 288 MDRN Hoxb5 Ebf2 Gly-Gaba 1
251 137 PH-an Pitx2 Glut 1
250 107 DMH Hmx2 Gaba 1
234 155 PRC-PAG Pax6 Glut 1
236 161 PAG Pou4f3 Glut 1
233 096 PVHd Gsc Gaba 1
126 257 SPVC Ccdc172 Glut 1
211 111 TRS-BAC Sln Glut 1
86 171 PAG Pou4f1 Bnc2 Glut 1
119 302 MV Xdh Gly-Gaba 1
111 185 SCig Tfap2b Chrnb3 Glut 1
104 262 Pineal Crx Glut 1
96 260 MDRNv Crp Glut 1
91 220 PB Pax5 Glut 1
88 248 MV-SPIV Zic4 Neurod2 Glut 1
84 133 PVH-SO-PVa Otp Glut 1
205 197 SNr Six3 Gaba 1
81 177 SCig-an-PPT Foxb1 Glut 1
54 303 IRN Dmbx1 Pax2 Gly-Gaba 1
53 187 SCsg Pde5a Glut 1
51 042 OB-out Frmd7 Gaba 1
39 160 PAG-SC Neurod2 Meis2 Glut 1
18 245 SPVI-SPVC Tlx3 Ebf3 Glut 1
120 301 MV Nr4a2 Gly-Gaba 1
122 218 PSV Lmx1a Trpv6 Glut 1
128 226 PRNc-PARN Tlx1 Glut 1
138 146 LH Pou4f1 Sox1 Glut 1
143 212 SCs Lef1 Gli3 Gaba 1
163 276 LDT-PCG St18 Gaba 1
164 099 SBPV-PVa Six6 Satb2 Gaba 1
175 309 CB PLI Gly-Gaba 1
178 044 OB Dopa-Gaba 1
181 310 CBX Golgi Gly-Gaba 1
187 021 L4 RSP-ACA Glut 1
188 312 CBX MLI Cdh22 Gaba 1
192 091 ARH-PVi Six6 Dopa-Gaba 1
194 307 RO-RPA Pkd2l1 Gaba 1
198 213 SCsg Gabrr2 Gaba 1
202 269 LDT Fgf7 Gaba 1
204 272 LDT-PCG-CS Gata3 Lhx1 Gaba 1
252 117 LHA Barhl2 Glut 1

4.3 Microglia (GFP-cre v.s. GFP)

Here, we use Wilcoxon rank-sum to compute differential expression in Microglia cells.

The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.

Cell number: ‘GFP’: 823, ‘GFP-cre’: 281.

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
499 Apoe -17.528004 -72.127530 0.0000000 0.0000000
480 Lgals3 -4.536480 -28.341877 0.0000057 0.0000540
497 Cd74 -16.465313 -19.163769 0.0000000 0.0000000
1 Selplg 16.442451 17.481213 0.0000000 0.0000000
2 Cx3cr1 15.344980 14.605617 0.0000000 0.0000000
6 Csf1r 11.373759 14.508338 0.0000000 0.0000000
0 Tmem119 16.584064 12.313411 0.0000000 0.0000000
498 C4b -16.541048 -8.793243 0.0000000 0.0000000
3 Camk2a 14.138077 7.035869 0.0000000 0.0000000
489 Spp1 -7.356597 -6.286214 0.0000000 0.0000000
493 Cst7 -9.361928 -6.133037 0.0000000 0.0000000
496 C3 -11.357290 -6.061773 0.0000000 0.0000000
483 Ctss -5.248227 -5.967553 0.0000002 0.0000017
469 Serpina3n -3.086549 -5.700789 0.0020249 0.0116376
484 Itgal -5.526251 -5.425139 0.0000000 0.0000004
487 Cxcl2 -6.669879 -4.750733 0.0000000 0.0000000
8 Hpca 8.956267 4.728704 0.0000000 0.0000000
495 Csf1 -9.549914 -4.433841 0.0000000 0.0000000
492 Gpc3 -8.764381 -4.430273 0.0000000 0.0000000
5 P2ry12 11.937934 4.316917 0.0000000 0.0000000
4 Siglech 13.443882 4.149309 0.0000000 0.0000000
490 Itgax -7.457363 -3.879903 0.0000000 0.0000000
478 Clec7a -4.175785 -3.712173 0.0000297 0.0002605
486 Xdh -6.638675 -3.633732 0.0000000 0.0000000
13 Syp 7.837777 3.564786 0.0000000 0.0000000
481 Ctsb -4.550565 -3.408067 0.0000054 0.0000525
20 Rph3a 6.482435 3.402979 0.0000000 0.0000000
491 Rgs12 -8.487657 -3.384927 0.0000000 0.0000000
14 Slc17a7 7.487700 3.303649 0.0000000 0.0000000
9 Cplx1 8.825599 3.252274 0.0000000 0.0000000
16 Syn1 7.200791 3.247201 0.0000000 0.0000000
482 Col6a1 -5.245410 -3.226926 0.0000002 0.0000017
17 Dnm1 7.082040 3.181284 0.0000000 0.0000000
55 Mrc2 3.091966 3.176309 0.0019884 0.0115602
52 Gm2115 3.202807 3.138704 0.0013609 0.0082985
494 Ly9 -9.499098 -3.092839 0.0000000 0.0000000
472 Egr2 -3.395019 -3.054615 0.0006862 0.0045147
488 Ddit3 -6.903155 -3.015658 0.0000000 0.0000000
476 Fmo1 -3.845645 -2.879638 0.0001202 0.0009393
18 Eno2 7.021473 2.878296 0.0000000 0.0000000
7 Dlg4 10.673281 2.744821 0.0000000 0.0000000
19 Nptxr 6.663053 2.616900 0.0000000 0.0000000
24 Nefm 5.845124 2.589533 0.0000000 0.0000001
15 Cd14 7.393870 2.519958 0.0000000 0.0000000
11 Trem2 8.236611 2.515758 0.0000000 0.0000000
25 Fam131a 5.676424 2.458847 0.0000000 0.0000002
477 Kit -4.057251 -2.457241 0.0000497 0.0004004
10 Bin1 8.631220 2.420129 0.0000000 0.0000000
49 Grin2b 3.255682 2.413346 0.0011312 0.0071595
475 Pdgfrb -3.687454 -2.394347 0.0002265 0.0016414
485 Gfap -6.031810 -2.383025 0.0000000 0.0000000
66 Cck 2.626606 2.343021 0.0086241 0.0431206
31 Gria2 4.640929 2.339874 0.0000035 0.0000347
468 Neu4 -3.034107 -2.295382 0.0024125 0.0135533
26 Grin1 5.509891 2.208000 0.0000000 0.0000004
59 Grin2a 2.914598 2.178512 0.0035615 0.0193558
12 Abi3 7.988383 2.163797 0.0000000 0.0000000
30 Gria1 4.849610 2.152534 0.0000012 0.0000126
58 Prkce 2.928359 2.142892 0.0034076 0.0187229
60 Nptx1 2.845038 2.141026 0.0044406 0.0238743
45 Cspg5 3.444427 2.079186 0.0005723 0.0039741
67 Vgf 2.620863 2.049634 0.0087707 0.0434196
34 Ecscr 4.245887 2.037883 0.0000218 0.0001944
43 Bsg 3.738053 2.031445 0.0001855 0.0013636
50 Adrb1 3.235854 2.008732 0.0012128 0.0075491
42 S100b 3.759615 2.003029 0.0001702 0.0012700
470 Atf3 -3.195331 -1.986412 0.0013967 0.0084139
39 Pecam1 3.956594 1.968960 0.0000760 0.0006034
47 Dkk3 3.398812 1.828204 0.0006768 0.0045120
479 Itpr2 -4.286410 -1.825444 0.0000182 0.0001651
22 Syngap1 6.062256 1.809762 0.0000000 0.0000000
32 Bcan 4.544823 1.807302 0.0000055 0.0000529
27 Tgfbr1 5.445206 1.792527 0.0000001 0.0000006
473 Cd83 -3.413114 -1.791534 0.0006423 0.0043395
54 Nnat 3.119595 1.783232 0.0018110 0.0106529
33 Rbfox3 4.478622 1.743174 0.0000075 0.0000696
53 Lynx1 3.183738 1.693879 0.0014539 0.0086540
471 Sulf2 -3.321992 -1.678094 0.0008938 0.0058037
57 App 2.976141 1.634580 0.0029190 0.0162167
64 Cpne6 2.719894 1.541622 0.0065303 0.0333177
36 Arc 4.104058 1.465963 0.0000406 0.0003440
29 Spi1 4.964568 1.396813 0.0000007 0.0000072
474 Bcl11b -3.664701 -1.330140 0.0002476 0.0017688
28 Mapt 5.120700 1.304393 0.0000003 0.0000032
21 Smad3 6.094761 1.279114 0.0000000 0.0000000
46 Cars 3.417990 1.256600 0.0006309 0.0043209
37 Slc29a1 4.081629 1.231171 0.0000447 0.0003712
23 Mink1 6.002989 1.213721 0.0000000 0.0000000
63 Adam10 2.744815 1.082109 0.0060545 0.0312088
467 Bcl6 -2.766701 -1.057593 0.0056627 0.0294930
40 Fam107a 3.778468 1.031091 0.0001578 0.0012138

4.4 Endothelia cells (GFP-cre v.s. GFP)

Here, we use Wilcoxon rank-sum to compute differential expression in Endothelia cells.

The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.

Cell number: ‘GFP-cre’: 604, ‘GFP’: 359}.

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
5 Bsg 10.653444 21.027288 0.0000000 0.0000000
9 Cldn5 8.154539 6.750578 0.0000000 0.0000000
499 Cd74 -8.856686 -5.983113 0.0000000 0.0000000
0 Flt1 13.857852 5.898455 0.0000000 0.0000000
493 Serpina3n -3.326124 -4.380862 0.0008806 0.0078627
2 Mfsd2a 12.394976 3.826172 0.0000000 0.0000000
11 Camk2a 8.049234 3.741868 0.0000000 0.0000000
4 Car4 10.844166 3.504257 0.0000000 0.0000000
1 Ctnnb1 12.959113 3.285085 0.0000000 0.0000000
31 Nefm 4.899336 3.278133 0.0000010 0.0000141
498 Ctss -6.017189 -3.232218 0.0000000 0.0000000
43 Agt 3.595075 3.195496 0.0003243 0.0032430
3 Klf2 10.876991 3.124009 0.0000000 0.0000000
24 App 5.366796 3.086241 0.0000001 0.0000015
17 Cplx1 6.886697 3.000003 0.0000000 0.0000000
496 C4b -4.576116 -2.965848 0.0000047 0.0000623
10 Rgs5 8.106259 2.892172 0.0000000 0.0000000
39 Slc17a7 3.925124 2.840441 0.0000867 0.0009851
497 Ppp1r1b -4.646199 -2.761572 0.0000034 0.0000470
21 Rph3a 6.049176 2.703232 0.0000000 0.0000000
6 Nos3 9.956928 2.617786 0.0000000 0.0000000
42 Olig1 3.602023 2.608540 0.0003158 0.0032219
45 Nnat 3.465212 2.580837 0.0005298 0.0050944
28 S100b 5.230343 2.511027 0.0000002 0.0000027
30 Gria1 4.916108 2.484843 0.0000009 0.0000134
8 Stard8 8.474764 2.339496 0.0000000 0.0000000
33 Ndnf 4.629307 2.231720 0.0000037 0.0000496
20 Bcan 6.056244 2.217539 0.0000000 0.0000000
495 C1qa -3.902841 -2.194318 0.0000951 0.0010563
23 Syp 5.461078 2.172042 0.0000000 0.0000009
491 Gfap -3.198178 -2.098706 0.0013830 0.0115249
47 Syn1 3.397285 2.076509 0.0006806 0.0061979
492 Penk -3.275449 -2.040568 0.0010549 0.0090943
40 Hpca 3.820059 2.027786 0.0001334 0.0014502
56 Ntrk2 2.847044 1.943510 0.0044127 0.0334297
7 Lef1 8.986549 1.924718 0.0000000 0.0000000
22 Pecam1 5.743446 1.908737 0.0000000 0.0000002
12 Klf4 7.963458 1.892956 0.0000000 0.0000000
35 Dnm1 4.233369 1.819683 0.0000230 0.0002878
41 Cspg5 3.796339 1.812952 0.0001468 0.0015622
14 Rapgef3 7.681569 1.723038 0.0000000 0.0000000
18 Gja1 6.333461 1.709328 0.0000000 0.0000000
13 Tek 7.846414 1.670759 0.0000000 0.0000000
38 Bin1 4.066847 1.630963 0.0000477 0.0005541
34 Eno2 4.473687 1.604909 0.0000077 0.0000986
53 Adam17 2.964209 1.595523 0.0030346 0.0240843
50 Mapt 3.210757 1.571966 0.0013239 0.0112191
19 Zbtb20 6.285900 1.508614 0.0000000 0.0000000
16 Rgs12 6.926111 1.493056 0.0000000 0.0000000
54 Synpo2 2.951750 1.460817 0.0031598 0.0246859
15 Degs2 6.965525 1.385835 0.0000000 0.0000000
29 Dlg4 5.222436 1.373153 0.0000002 0.0000028
60 Fam131a 2.701368 1.336147 0.0069055 0.0493250
494 Bgn -3.604300 -1.297905 0.0003130 0.0032219
25 Sema3c 5.358649 1.265677 0.0000001 0.0000015
58 Trpm4 2.747611 1.236203 0.0060031 0.0435805
27 Mink1 5.310250 1.208434 0.0000001 0.0000018
36 Fermt2 4.151425 1.206600 0.0000330 0.0004006
48 Map4k3 3.396806 1.186127 0.0006818 0.0061979
37 Tshz1 4.147233 1.123684 0.0000337 0.0004006
49 Fn1 3.320493 1.099788 0.0008986 0.0078823
26 Cdh5 5.336246 1.084284 0.0000001 0.0000016
51 Lynx1 3.090478 1.031523 0.0019983 0.0163799
32 Adgrl2 4.731137 1.028183 0.0000022 0.0000319

4.5 CA1 Glut (GFP-cre v.s. GFP)

Here, we use Wilcoxon rank-sum to compute differential expression in CA1 Glut cells.

The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.

Cell number: ‘GFP-cre’: 674, ‘GFP’: 71.

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
4 Hpca 6.087094 16.628431 0.0000000 0.0000001
19 Gria1 3.828857 14.512842 0.0001287 0.0025497
0 Fam131a 7.402612 12.221754 0.0000000 0.0000000
9 Camk2a 4.836512 10.497404 0.0000013 0.0000508
5 Syp 5.781551 10.092332 0.0000000 0.0000004
29 Slc17a7 3.487368 8.949147 0.0004878 0.0062539
1 Fibcd1 6.948065 7.037974 0.0000000 0.0000000
25 Grin2a 3.578683 6.993995 0.0003453 0.0049333
499 Ctss -6.984012 -6.956723 0.0000000 0.0000000
18 Grin2b 3.958147 6.953647 0.0000755 0.0016420
23 Dkk3 3.670288 6.925179 0.0002423 0.0036570
497 Cd74 -6.320455 -6.898205 0.0000000 0.0000000
7 Cx3cl1 4.904636 6.805468 0.0000009 0.0000425
13 Egr1 4.222237 6.428306 0.0000242 0.0006633
2 Kcnab1 6.723691 6.342738 0.0000000 0.0000000
3 Bcan 6.148261 5.659902 0.0000000 0.0000001
22 Cpne6 3.692899 5.658398 0.0002217 0.0036543
30 Ptk2b 3.292852 5.071836 0.0009918 0.0123971
498 Gfap -6.401044 -4.912414 0.0000000 0.0000000
17 Eno2 3.997863 4.891961 0.0000639 0.0014527
20 Wfs1 3.826538 4.763576 0.0001300 0.0025497
12 Egr4 4.594454 3.710779 0.0000043 0.0001276
15 Rbfox3 4.129182 3.578949 0.0000364 0.0009101
32 Zbtb20 3.116020 3.459279 0.0018331 0.0213151
490 Cxcl10 -3.235744 -3.423799 0.0012133 0.0147959
494 Col6a1 -3.787983 -3.412698 0.0001519 0.0027343
10 Kcnd2 4.802015 3.324475 0.0000016 0.0000561
21 Syn1 3.776677 3.136939 0.0001589 0.0027403
495 Sulf2 -3.821610 -3.003816 0.0001326 0.0025497
6 Prkce 5.008996 2.850744 0.0000005 0.0000274
14 Itga7 4.212960 2.780114 0.0000252 0.0006633
26 Mink1 3.564768 2.776180 0.0003642 0.0050580
8 Cck 4.845789 2.774319 0.0000013 0.0000508
11 Nefm 4.603731 2.518946 0.0000041 0.0001276
492 Dclk3 -3.687391 -2.135854 0.0002266 0.0036543
491 C1qa -3.675506 -2.089087 0.0002374 0.0036570
34 Neurod6 3.004702 2.080610 0.0026584 0.0295379
16 Htr1a 4.051492 2.009620 0.0000509 0.0012117
35 Adrb1 2.940926 1.941880 0.0032723 0.0355687
27 Npy2r 3.509979 1.940219 0.0004481 0.0059547
496 Csf1r -4.693017 -1.797835 0.0000027 0.0000897
28 Bcl11b 3.507370 1.779664 0.0004526 0.0059547
31 Kcnh7 3.179505 1.699659 0.0014753 0.0175627
24 Bcl6 3.663620 1.670695 0.0002487 0.0036570
493 Adgrl2 -3.785954 -1.588879 0.0001531 0.0027343
33 Pcdhgc5 3.064129 1.395493 0.0021830 0.0248073

4.6 CA3 Glut (GFP-cre v.s. GFP)

Here, we use Wilcoxon rank-sum to compute differential expression in CA3 Glut cells.

The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

In volcano plot, log10(p_adj) > -25 and log10(p_adj) < -5 is shown.

Cell number: ‘GFP-cre’: 594, ‘GFP’: 153.

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
5 Slc17a7 13.829126 32.785248 0.0000000 0.0000000
142 Osr1 2.956992 27.985668 0.0031066 0.0106389
7 Gria1 13.361713 22.486418 0.0000000 0.0000000
2 Cpne6 14.999445 20.781628 0.0000000 0.0000000
19 Dnm1 10.683278 19.660599 0.0000000 0.0000000
11 Hpca 12.699142 18.664454 0.0000000 0.0000000
1 Camk2a 15.103851 18.596859 0.0000000 0.0000000
0 Syp 15.162251 18.328075 0.0000000 0.0000000
18 Nptx1 11.201529 16.613106 0.0000000 0.0000000
3 Ptk2b 14.384350 16.052973 0.0000000 0.0000000
4 Gria2 14.248222 14.505323 0.0000000 0.0000000
59 Nptxr 6.947125 12.231750 0.0000000 0.0000000
93 App 4.741565 11.933023 0.0000021 0.0000110
37 Dkk3 8.927485 10.880051 0.0000000 0.0000000
49 Zbtb20 7.788888 9.195160 0.0000000 0.0000000
6 Eno2 13.470531 9.061977 0.0000000 0.0000000
12 Bin1 12.509446 8.787798 0.0000000 0.0000000
8 Rph3a 13.161094 8.698674 0.0000000 0.0000000
15 Grin2a 11.632810 8.612867 0.0000000 0.0000000
45 Syngap1 8.303568 8.133543 0.0000000 0.0000000
10 Fam131a 12.742837 7.894958 0.0000000 0.0000000
76 Grin1 5.779537 7.491878 0.0000000 0.0000000
44 Sema5b 8.418057 7.032755 0.0000000 0.0000000
50 Neurod6 7.766830 7.016976 0.0000000 0.0000000
26 Grin2b 9.860842 6.775390 0.0000000 0.0000000
47 Bcan 7.991399 6.737943 0.0000000 0.0000000
9 Cx3cl1 13.137355 6.619198 0.0000000 0.0000000
14 Cck 11.646045 6.614101 0.0000000 0.0000000
41 Itga7 8.680860 6.470300 0.0000000 0.0000000
38 Syn1 8.926645 6.377339 0.0000000 0.0000000
36 Plxna1 8.990928 5.956524 0.0000000 0.0000000
121 Fezf2 3.805688 5.862751 0.0001414 0.0005702
13 Mink1 11.719150 5.822962 0.0000000 0.0000000
71 Car4 6.112503 5.749875 0.0000000 0.0000000
34 Robo1 9.132307 5.711690 0.0000000 0.0000000
134 Cckbr 3.291008 5.668843 0.0009983 0.0036170
32 Rbfox3 9.310239 5.637467 0.0000000 0.0000000
91 Iyd 4.828535 5.586290 0.0000014 0.0000074
42 Mapt 8.654390 5.485796 0.0000000 0.0000000
156 Col11a1 2.482646 5.171348 0.0130410 0.0404642
39 Cspg5 8.821818 5.129020 0.0000000 0.0000000
24 Neto1 9.887731 5.117392 0.0000000 0.0000000
64 Arc 6.766461 5.068835 0.0000000 0.0000000
94 Nectin3 4.719087 5.046242 0.0000024 0.0000122
113 Scn4b 4.013661 5.002230 0.0000598 0.0002577
23 Pcdh9 10.425519 4.931618 0.0000000 0.0000000
25 Pkp2 9.877857 4.892412 0.0000000 0.0000000
60 Brinp1 6.897337 4.834978 0.0000000 0.0000000
17 Ctnnb1 11.233460 4.821881 0.0000000 0.0000000
30 Npy2r 9.496574 4.758524 0.0000000 0.0000000
499 Col6a1 -11.018556 -4.749074 0.0000000 0.0000000
21 Prkce 10.568579 4.696455 0.0000000 0.0000000
157 Crebbp 2.480756 4.675079 0.0131104 0.0404642
55 Chrna7 7.352776 4.624490 0.0000000 0.0000000
29 Gpr158 9.515271 4.610660 0.0000000 0.0000000
54 Camk4 7.430083 4.577786 0.0000000 0.0000000
33 Gria3 9.234612 4.560895 0.0000000 0.0000000
61 Sulf2 6.860994 4.472543 0.0000000 0.0000000
46 Nrg3 8.218489 4.466240 0.0000000 0.0000000
22 Src 10.440014 4.456206 0.0000000 0.0000000
35 Lynx1 9.101847 4.454622 0.0000000 0.0000000
16 Kcnc1 11.360765 4.444184 0.0000000 0.0000000
132 Gpr63 3.330292 4.426542 0.0008675 0.0031895
72 Nos1 6.109142 4.360443 0.0000000 0.0000000
28 Kcnd2 9.596569 4.238446 0.0000000 0.0000000
53 Rims1 7.543943 4.201822 0.0000000 0.0000000
128 Sox8 3.504653 4.187573 0.0004572 0.0017318
40 Cplx1 8.732958 4.162605 0.0000000 0.0000000
98 Trpm4 4.628545 4.137064 0.0000037 0.0000182
154 Olig1 2.512057 4.101265 0.0120030 0.0379841
140 Enpp2 3.115177 4.074431 0.0018383 0.0063831
80 Sstr3 5.577446 4.055631 0.0000000 0.0000001
52 Plp1 7.716623 4.055600 0.0000000 0.0000000
115 Epha10 3.982990 4.033365 0.0000681 0.0002884
143 Rspo2 2.893340 3.943844 0.0038117 0.0129649
97 Nr4a2 4.648292 3.922088 0.0000033 0.0000167
123 Cdh9 3.754220 3.891115 0.0001739 0.0006846
139 Kcnh2 3.118328 3.880388 0.0018188 0.0063594
136 Cpne5 3.212231 3.869599 0.0013171 0.0047039
20 Pcdhgc5 10.653658 3.854878 0.0000000 0.0000000
145 Tnik 2.807210 3.847019 0.0049973 0.0167694
111 Adrb1 4.096850 3.813079 0.0000419 0.0001837
131 Npy1r 3.334494 3.723292 0.0008545 0.0031650
152 Ptpru 2.532854 3.711539 0.0113138 0.0362622
75 Prkcd 5.801805 3.708364 0.0000000 0.0000000
89 Dlg4 4.936303 3.690283 0.0000008 0.0000044
73 Gng2 5.921967 3.685230 0.0000000 0.0000000
112 Plcxd2 4.080674 3.657899 0.0000449 0.0001952
27 Ntng2 9.661061 3.657227 0.0000000 0.0000000
137 Bace1 3.142277 3.639369 0.0016764 0.0059447
58 Lrpprc 7.116444 3.603572 0.0000000 0.0000000
51 Pcdhac2 7.733429 3.503662 0.0000000 0.0000000
82 Egr1 5.417160 3.460430 0.0000001 0.0000004
84 Psen2 5.365693 3.451159 0.0000001 0.0000005
108 Prox1 4.163023 3.403410 0.0000314 0.0001415
43 Camk2g 8.542842 3.382412 0.0000000 0.0000000
86 Mapk1 5.039449 3.370589 0.0000005 0.0000027
99 Nr4a1 4.620143 3.363748 0.0000038 0.0000188
65 Epha7 6.750706 3.333398 0.0000000 0.0000000
70 Gja1 6.173004 3.330926 0.0000000 0.0000000
92 Grm1 4.752699 3.327219 0.0000020 0.0000106
81 Rims2 5.499509 3.322733 0.0000000 0.0000002
31 Sorl1 9.407713 3.253944 0.0000000 0.0000000
138 Grm3 3.139756 3.194886 0.0016909 0.0059538
90 Tbr1 4.887356 3.131626 0.0000010 0.0000056
79 Mas1 5.665257 3.087153 0.0000000 0.0000001
147 S100b 2.664990 3.065911 0.0076991 0.0254936
109 Gabra1 4.147267 3.030323 0.0000336 0.0001502
57 Myo5a 7.211607 3.029945 0.0000000 0.0000000
77 Map4k3 5.755588 3.011587 0.0000000 0.0000001
48 Grb2 7.859683 2.998926 0.0000000 0.0000000
78 Bsg 5.728069 2.974316 0.0000000 0.0000001
107 Fermt2 4.195374 2.879404 0.0000272 0.0001238
117 Rasgrf2 3.939715 2.845032 0.0000816 0.0003399
148 Gad2 2.609111 2.843162 0.0090778 0.0298612
110 Ntrk2 4.104622 2.839644 0.0000405 0.0001792
69 Pdgfa 6.245059 2.833634 0.0000000 0.0000000
85 Kctd4 5.224313 2.665583 0.0000002 0.0000010
87 Slc29a1 4.996594 2.631637 0.0000006 0.0000033
66 Gphn 6.689364 2.594312 0.0000000 0.0000000
103 Crhr1 4.368895 2.574274 0.0000125 0.0000589
133 Ngrn 3.297311 2.550913 0.0009762 0.0035626
116 Cnr1 3.956941 2.532146 0.0000759 0.0003190
56 Ctsb 7.285973 2.512189 0.0000000 0.0000000
141 Slc29a2 3.096061 2.481938 0.0019611 0.0067624
62 Tcerg1 6.854902 2.480017 0.0000000 0.0000000
102 Nnat 4.511535 2.445188 0.0000064 0.0000306
119 Pcdhgc3 3.873332 2.340500 0.0001074 0.0004400
101 Car12 4.526450 2.317656 0.0000060 0.0000288
83 Psen1 5.398464 2.302720 0.0000001 0.0000004
88 Cars 4.978948 2.294152 0.0000006 0.0000036
63 Kcnab1 6.844819 2.268631 0.0000000 0.0000000
149 Gpr83 2.601968 2.247424 0.0092690 0.0302910
67 Mtor 6.602184 2.230910 0.0000000 0.0000000
114 Syt17 3.997065 2.218328 0.0000641 0.0002741
74 Smad3 5.812939 2.204646 0.0000000 0.0000000
100 Tmem150a 4.587791 2.203672 0.0000045 0.0000217
104 Lct 4.342636 2.200770 0.0000141 0.0000658
122 Kit 3.767665 2.196521 0.0001648 0.0006539
496 Cd74 -2.507225 -2.167152 0.0121683 0.0382652
106 Bcl11b 4.239070 2.148576 0.0000224 0.0001030
118 Plekhg1 3.930892 2.075926 0.0000846 0.0003497
158 Adam10 2.428868 2.060257 0.0151461 0.0464603
155 Rgs12 2.504494 2.050973 0.0122627 0.0383208
498 Dclk3 -4.787781 -2.020220 0.0000017 0.0000090
153 Ccl6 2.529283 1.987903 0.0114296 0.0364000
129 Lmna 3.393734 1.812827 0.0006895 0.0025920
120 Fam107a 3.812831 1.780631 0.0001374 0.0005585
68 Dapk1 6.307662 1.722117 0.0000000 0.0000000
151 Gria4 2.540206 1.710254 0.0110787 0.0357377
127 Nrg2 3.574608 1.693545 0.0003508 0.0013388
124 Wfs1 3.709685 1.626378 0.0002075 0.0008106
96 Nrn1 4.681694 1.624039 0.0000028 0.0000144
146 Lratd2 2.672553 1.602593 0.0075277 0.0250922
144 Csf1 2.852796 1.516918 0.0043336 0.0146407
126 Crtac1 3.592254 1.436591 0.0003278 0.0012609
135 Adgra1 3.285967 1.422559 0.0010163 0.0036559
95 Snca 4.687156 1.412891 0.0000028 0.0000141
125 Sharpin 3.625866 1.399960 0.0002880 0.0011163
130 Bdnf 3.384281 1.253605 0.0007136 0.0026629
150 Gad1 2.550920 1.208437 0.0107439 0.0348828
497 Serpina3n -3.777959 -1.118605 0.0001581 0.0006325

Abbreviation

Cell types & Regions

Astro, Astrocyte;

ABC, arachnoid barrier cells;

BAM, border-associated macrophages;

BLA, Basolateral amygdala;

CB, cerebellum;

CGE, caudal ganglionic eminence;

CHOR, choroid plexus;

CNU, cerebral nuclei;

CR, Cajal–Retzius;

CT, corticothalamic;

CTX, cerebral cortex;

CTXsp, cortical subplate;

DC, dendritic cells;

DCO, dorsal cochlear nucleus;

DG, dentate gyrus;

EA, extended amygdala;

Endo, endothelial cells;

ENT, Entorhinal area;

ENTl, Entorhinal area, lateral part;

Epen, ependymal;

EPI, epithalamus;

ET, extratelencephalic;

GC, granule cell;

HB, hindbrain;

HPF, hippocampal formation;

HY, hypothalamus;

HYa, anterior hypothalamic;

IMN, immature neurons;

IT, intratelencephalic;

L6b, layer 6b;

LGE, lateral ganglionic eminence;

LH, lateral habenula;

LSX, lateral septal complex;

MB, midbrain;

MGE, medial ganglionic eminence;

MH, medial habenula;

MM, medial mammillary nucleus;

MY, medulla;

NN, non-neuronal;

NP, near-projecting;

NT, non-telencephalon;

OB, olfactory bulb;

OEC, olfactory ensheathing cells;

OLF, olfactory areas;

Oligo, oligodendrocytes;

OPC, oligodendrocyte precursor cells;

P, pons;

PAL, pallidum;

Peri, pericytes;

PIR, piriform cortex;

SMC, smooth muscle cells;

STR, striatum;

TE, telencephalon;

TH, thalamus;

UBC, unipolar brush cells;

VLMC, vascular leptomeningeal cells.

Neurotransmitter types

Chol, cholinergic;

Dopa, dopaminergic;

GABA, GABAergic;

Glut, glutamatergic;

Glyc, glycinergic;

Hist, histaminergic;

Nora, noradrenergic;

Sero, serotonergic